R Notebook

Continuing my expolartion of Notification of Infectious Disease data

https://journocode.com/2016/01/28/your-first-choropleth-map/

library("rgdal")
LocalAuthorities<-readOGR("https://opendata.arcgis.com/datasets/686603e943f948acaa13fb5d2b0f1275_4.geojson")

OGR data source with driver: GeoJSON 
Source: "https://opendata.arcgis.com/datasets/686603e943f948acaa13fb5d2b0f1275_4.geojson", layer: "686603e943f948acaa13fb5d2b0f1275_4"
with 380 features
It has 10 fields

“Statutory notifiable diseases - number of cases reported in week 51 of 2017”

library("reshape2")
library("magrittr")
geo_disease_data<-read.csv("geo_disease_data.csv")
geo_disease_data[is.na(geo_disease_data)] <- 0
geo_disease_data$LocalAuthority<-gsub(" UA", "", geo_disease_data$LocalAuthority)
LA_Diseases<-sp::merge(LocalAuthorities, geo_disease_data, by.x="lad16nm", by.y="LocalAuthority")

library("leaflet")
diseases <- names(geo_disease_data)[-1]
max_cases <- max(melt(geo_disease_data)$value)

Using LocalAuthority as id variables

pal <- colorNumeric(
   palette = "viridis",
   domain = c(0,max_cases)
 )
myleaflet<-leaflet(width = "100%") %>% 
  addProviderTiles("Esri.WorldGrayCanvas") %>%
  addLegend( pal = pal, 
             values = 0:max_cases,
             title = "Cases",
             opacity = 1) %>%
  addLayersControl(baseGroups=diseases, 
                   position = "bottomleft", 
                   options = layersControlOptions(collapsed = FALSE))
for (active_disease in diseases) 
  {
  myleaflet <- myleaflet %>%
    addPolygons(data=LA_Diseases, 
              fillColor=~pal(LA_Diseases[[active_disease]]),
              fillOpacity = 0.8,
              color = "black",
              weight = 1,
              popup = paste(LA_Diseases$lad16nm, LA_Diseases[[active_disease]],"cases"),
              group = active_disease
              )
  }    
myleaflet

Unique_LA_Map<-data.frame(LocalAuthority=unique(LocalAuthorities$lad16nm) %>% sort())
Unique_LA_Diseases<-data.frame(LocalAuthority=unique(geo_disease_data$LocalAuthority) %>% sort())
In_Map_Not_Diseases<-data.frame(LocalAuthority=
  Unique_LA_Map$LocalAuthority[!(Unique_LA_Map$LocalAuthority %in% Unique_LA_Diseases$LocalAuthority)])
In_Diseases_Not_Map<-data.frame(LocalAuthority=
  Unique_LA_Diseases$LocalAuthority[!(Unique_LA_Diseases$LocalAuthority %in% Unique_LA_Map$LocalAuthority)])